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Zimowska GJ, Xavier N, Qadri M, Handler AM. A transposon-based genetic marker for conspecific identity within the Bactrocera dorsalis species complex. Sci Rep 2024; 14:1924. [PMID: 38253542 PMCID: PMC10803768 DOI: 10.1038/s41598-023-51068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Here we describe a molecular approach to assess conspecific identity that relies on the comparison of an evolved mutated transposable element sequence and its genomic insertion site in individuals from closely related species. This was explored with the IFP2 piggyBac transposon, originally discovered in Trichoplusia ni as a 2472 bp functional element, that was subsequently found as mutated elements in seven species within the Bactrocera dorsalis species complex. In a B. dorsalis [Hendel] strain collected in Kahuku, Hawaii, a degenerate 2420 bp piggyBac sequence (pBacBd-Kah) having ~ 94.5% sequence identity to IFP2 was isolated, and it was reasoned that common species, or strains within species, should share the same evolved element and its precise genomic insertion site. To test this assumption, PCR using primers to pBacBd-Kah and adjacent genomic sequences was used to isolate and compare homologous sequences in strains of four sibling species within the complex. Three of these taxa, B. papayae, B. philippinensis, and B. invadens, were previously synonymized with B. dorsalis, and found to share nearly identical pBacBd-Kah homologous elements (> 99% nucleotide identity) within the identical insertion site consistent with conspecific species. The fourth species tested, B. carambolae, considered to be a closely related yet independent species sympatric with B. dorsalis, also shared the pBacBd-Kah sequence and insertion site in one strain from Suriname, while another divergent pBacBd-Kah derivative, closer in identity to IFP2, was found in individuals from French Guiana, Bangladesh and Malaysia. This data, along with the absence of pBacBd-Kah in distantly related Bactrocera, indicates that mutated descendants of piggyBac, as well as other invasive mobile elements, could be reliable genomic markers for common species identity.
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Affiliation(s)
- Grazyna J Zimowska
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Nirmala Xavier
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Masroor Qadri
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Alfred M Handler
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA.
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2
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Hua WK, Hsu JC, Chen YC, Chang PS, Wen KLK, Wang PN, Yang WC, Shen CN, Yu YS, Chen YC, Cheng IC, Wu SCY. Quantum pBac: An effective, high-capacity piggyBac-based gene integration vector system for unlocking gene therapy potential. FASEB J 2023; 37:e23108. [PMID: 37534940 DOI: 10.1096/fj.202201654r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/02/2023] [Accepted: 07/12/2023] [Indexed: 08/04/2023]
Abstract
Recent advances in gene therapy have brought novel treatment options for cancer. However, the full potential of this approach has yet to be unlocked due to the limited payload capacity of commonly utilized viral vectors. Virus-free DNA transposons, including piggyBac, have the potential to obviate these shortcomings. In this study, we improved a previously modified piggyBac system with superior transposition efficiency. We demonstrated that the internal domain sequences (IDS) within the 3' terminal repeat domain of hyperactive piggyBac (hyPB) donor vector contain dominant enhancer elements. Plasmid-free donor vector devoid of IDS was used in conjunction with a helper plasmid expressing Quantum PBase™ v2 to generate an optimal piggyBac system, Quantum pBac™ (qPB), for use in T cells. qPB outperformed hyPB in CD20/CD19 CAR-T production in terms of performance as well as yield of the CAR-T cells produced. Furthermore, qPB also produced CAR-T cells with lower donor-associated variabilities compared to lentiviral vector. Importantly, qPB yielded mainly CD8+ CAR-TSCM cells, and the qPB-produced CAR-T cells effectively eliminated CD20/CD19-expressing tumor cells both in vitro and in vivo. Our findings confirm qPB as a promising virus-free vector system with an enhanced payload capacity to incorporate multiple genes. This highly efficient and potentially safe system will be expected to further advance gene therapy applications.
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Affiliation(s)
- Wei-Kai Hua
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Jeff C Hsu
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Yi-Chun Chen
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Peter S Chang
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | | | - Po-Nan Wang
- Division of Hematology, Chang Gung Medical Foundation, Taipei City, Taiwan ROC
| | - Wei-Cheng Yang
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan ROC
| | - Chia-Ning Shen
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan ROC
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan ROC
| | - Yi-Shan Yu
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Ying-Chun Chen
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - I-Cheng Cheng
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
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3
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Redd PS, Diaz S, Weidner D, Benjamin J, Hancock CN. Mobility of mPing and its associated elements is regulated by both internal and terminal sequences. Mob DNA 2023; 14:1. [PMID: 36774502 PMCID: PMC9921582 DOI: 10.1186/s13100-023-00289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/04/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND DNA transposable elements are mobilized by a "cut and paste" mechanism catalyzed by the binding of one or more transposase proteins to terminal inverted repeats (TIRs) to form a transpositional complex. Study of the rice genome indicates that the mPing element has experienced a recent burst in transposition compared to the closely related Ping and Pong elements. A previously developed yeast transposition assay allowed us to probe the role of both internal and terminal sequences in the mobilization of these elements. RESULTS We observed that mPing and a synthetic mPong element have significantly higher transposition efficiency than the related autonomous Ping and Pong elements. Systematic mutation of the internal sequences of both mPing and mPong identified multiple regions that promote or inhibit transposition. Simultaneous alteration of single bases on both mPing TIRs resulted in a significant reduction in transposition frequency, indicating that each base plays a role in efficient transposase binding. Testing chimeric mPing and mPong elements verified the important role of both the TIRs and internal regulatory regions. Previous experiments showed that the G at position 16, adjacent to the 5' TIR, allows mPing to have higher mobility. Alteration of the 16th and 17th base from mPing's 3' end or replacement of the 3' end with Pong 3' sequences significantly increased transposition frequency. CONCLUSIONS As the transposase proteins were consistent throughout this study, we conclude that the observed transposition differences are due to the element sequences. The presence of sub-optimal internal regions and TIR bases supports a model in which transposable elements self-limit their activity to prevent host damage and detection by host regulatory mechanisms. Knowing the role of the TIRs, adjacent sub-TIRs, and internal regulatory sequences allows for the creation of hyperactive elements.
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Affiliation(s)
- Priscilla S. Redd
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA
| | - Stephanie Diaz
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA ,grid.66859.340000 0004 0546 1623Present address: Bayer Pharmaceuticals, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - David Weidner
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA
| | - Jazmine Benjamin
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA ,grid.265892.20000000106344187Present address: Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - C. Nathan Hancock
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA
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4
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Hu G, Song M, Wang Y, Hao K, Wang J, Zhang Y. Using a modified piggyBac transposon-combined Cre/loxP system to produce selectable reporter-free transgenic bovine mammary epithelial cells for somatic cell nuclear transfer. Genesis 2023:e23510. [PMID: 36748563 DOI: 10.1002/dvg.23510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Transposon systems are widely used for genetic engineering in various model organisms. PiggyBac (PB) has recently been confirmed to have highly efficient transposition in the mouse germ line and mammalian cell lines. In this study, we used a modified PB transposon system mediated by PB transposase (PBase) mRNA carrying the human lactoferrin gene driven by bovine β-casein promoter to transfect bovine mammary epithelial cells (BMECs), and the selectable reporter in two stable transgenic BMEC clones was removed using cell-permeant Cre recombinase. These reporter-free transgenic BMECs were used as donor cells for somatic cell nuclear transfer (SCNT) and exhibited a competence of SCNT embryos similar to stable transgenic BMECs and nontransgenic BMECs. The comprehensive information from this study provided a modified approach using an altered PB transposon system mediated by PBase mRNA in vitro and combined with the Cre/loxP system to produce transgenic and selectable reporter-free donor nuclei for SCNT. Consequently, the production of safe bovine mammary bioreactors can be promoted.
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Affiliation(s)
- Guangdong Hu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Meijun Song
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yan Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Kexing Hao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jing Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
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5
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Lalli M, Yen A, Thopte U, Dong F, Moudgil A, Chen X, Milbrandt J, Dougherty JD, Mitra RD. Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes. NAR Genom Bioinform 2022; 4:lqac061. [PMID: 36062164 PMCID: PMC9428926 DOI: 10.1093/nargab/lqac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/04/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Calling cards technology using self-reporting transposons enables the identification of DNA-protein interactions through RNA sequencing. Although immensely powerful, current implementations of calling cards in bulk experiments on populations of cells are technically cumbersome and require many replicates to identify independent insertions into the same genomic locus. Here, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells by introducing a DNA barcode into the calling card itself. An additional barcode incorporated during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recover in vitro binding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2 and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. Lastly, we demonstrated barcoded calling cards can record binding in vivo in the mouse brain. In sum, RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is an efficient and powerful method to infer gene regulatory networks in a population of cells.
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Affiliation(s)
- Matthew Lalli
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allen Yen
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Urvashi Thopte
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fengping Dong
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Arnav Moudgil
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Xuhua Chen
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robi D Mitra
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
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6
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Hamad S, Derichsweiler D, Hescheler J, Pfannkuche K. Scalable Generation of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2454:145-161. [PMID: 34664217 DOI: 10.1007/7651_2021_395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) can be expanded at limitless scale in vitro and give rise to various organotypic cells, cardiomyocytes (CMs) among them. Advanced protocols shape the differentiation process of pluripotent stem cells by controlled growth factor application. Modulating the Wnt signaling pathway is effective to direct hiPSCs to CMs (hiPSC-CMs) and native growth factors were replaced by small chemical compounds. Here, we describe a refined protocol for scalable generation of hiPSC-CMs that manipulates porcupine and tankyrase sub-pathways of Wnt signaling for tight inhibition of non-canonical Wnt signaling. The approach results in a differentiation efficiency toward hiPSC-CMs of 87 ± 0.9% in stirred bioreactor cultures and yields about 70 million hiPSC-CMs per 100 mL serum free cardiac differentiation medium. The differentiation protocol is easily adapted from 3D to 2D culture and vice versa and has been demonstrated to work with different hiPSC lines.
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Affiliation(s)
- Sarkawt Hamad
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, University of Cologne, Medical Faculty, Cologne, Germany.,Biology Department, Faculty of Science, Soran University, Soran, Kurdistan Region, Iraq
| | - Daniel Derichsweiler
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, University of Cologne, Medical Faculty, Cologne, Germany
| | - Jürgen Hescheler
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, University of Cologne, Medical Faculty, Cologne, Germany
| | - Kurt Pfannkuche
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, University of Cologne, Medical Faculty, Cologne, Germany. .,Department of Pediatric Cardiology, University Clinics of Cologne, Cologne, Germany. .,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany. .,Marga-and-Walter-Boll Laboratory for Cardiac Tissue Engineering, University of Cologne, Cologne, Germany.
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7
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Vierl F, Kaur M, Götz M. Non-codon Optimized PiggyBac Transposase Induces Developmental Brain Aberrations: A Call for in vivo Analysis. Front Cell Dev Biol 2021; 9:698002. [PMID: 34414186 PMCID: PMC8369470 DOI: 10.3389/fcell.2021.698002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
In this perspective article, we briefly review tools for stable gain-of-function expression to explore key fate determinants in embryonic brain development. As the piggyBac transposon system has the highest insert size, a seamless integration of the transposed sequence into the host genome, and can be delivered by transfection avoiding viral vectors causing an immune response, we explored its use in the murine developing forebrain. The original piggyBac transposase PBase or the mouse codon-optimized version mPB and the construct to insert, contained in the piggyBac transposon, were introduced by in utero electroporation at embryonic day 13 into radial glia, the neural stem cells, in the developing dorsal telencephalon, and analyzed 3 or 5 days later. When using PBase, we observed an increase in basal progenitor cells, often accompanied by folding aberrations. These effects were considerably ameliorated when using the piggyBac plasmid together with mPB. While size and strength of the electroporated region was not correlated to the aberrations, integration was essential and the positive correlation to the insert size implicates the frequency of transposition as a possible mechanism. We discuss this in light of the increase in transposing endogenous viral vectors during mammalian phylogeny and their role in neurogenesis and radial glial cells. Most importantly, we aim to alert the users of this system to the phenotypes caused by non-codon optimized PBase application in vivo.
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Affiliation(s)
- Franziska Vierl
- Institute for Stem Cell Research, Helmholtz Zentrum München, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany.,Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Manpreet Kaur
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany.,SyNergy, Munich Cluster for Systems Neurology, Ludwig-Maximilians-Universität, Munich, Germany
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8
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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9
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Masalmeh RHA, Taglini F, Rubio-Ramon C, Musialik KI, Higham J, Davidson-Smith H, Kafetzopoulos I, Pawlicka KP, Finan HM, Clark R, Wills J, Finch AJ, Murphy L, Sproul D. De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands. Nat Commun 2021; 12:694. [PMID: 33514701 PMCID: PMC7846778 DOI: 10.1038/s41467-020-20716-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The aberrant gain of DNA methylation at CpG islands is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CpG islands are targeted by de novo DNA methyltransferases in a sequence-specific manner, but this has not been tested. Using ectopically integrated CpG islands, here we find that aberrantly methylated CpG islands are subject to low levels of de novo DNA methylation activity in colorectal cancer cells. By delineating DNA methyltransferase targets, we find that instead de novo DNA methylation activity is targeted primarily to CpG islands marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CpG islands are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNA methyltransferase activity at CpG islands in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.
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Affiliation(s)
| | - Francesca Taglini
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kamila I Musialik
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Jonathan Higham
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kamila P Pawlicka
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Hannah M Finan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Richard Clark
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Andrew J Finch
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK.
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10
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Hu H, Zhang Z, Wang R, Wang Y, Jin J, Cai L, Yang J, Duan H, Wu Z, Fang Z, Liu B. BGC823 Cell Line with the Stable Expression of iRFP720 Retains Its Primary Properties with Promising Fluorescence Imaging Ability. DNA Cell Biol 2020; 39:900-908. [PMID: 32096664 DOI: 10.1089/dna.2019.5057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reliable animal models are required for understanding the molecular events of gastric tumor growth and metastasis. Tracing techniques based on iRFP720 may optimize the noninvasive monitoring of tumors in vivo. The present study established a human gastric adenocarcinoma cell line BGC823-iRFP720-GFP (abbreviated as BGC823-iRFP) that stably expressed iRFP720 and green fluorescent protein (GFP) by piggyBac transposon system. The monoclonal cell line BGC823-iRFP was isolated under puromycin selection. The cell morphology and proliferation ability of BGC823-iRFP cells in vitro were similar to that of the BGC823 cells. The iRFP720 and GFP expressions were confirmed by laser confocal microscopy and Cytation™ 5. Hematoxylin and eosin staining, immunohistochemical analysis, and animal experiments also revealed that BGC823-iRFP exhibited no significant changes in morphology, growth kinetics, and tumorigenicity in vivo. IVIS Lumina III imaging indicated that the iRFP720 signals of the BGC823-iRFP cells could be used to evaluate the antitumor efficacy of oncolytic viruses and chemotherapy drugs. Therefore, the BGC823-iRFP cells would be a useful tool for gastric cancer research and antitumor drug evaluation.
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Affiliation(s)
- Han Hu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Ziyi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Runyang Wang
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | - Yang Wang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Jing Jin
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | - Linkang Cai
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | - Junhan Yang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Haixiao Duan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Zhen Wu
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | | | - Binlei Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China.,Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
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11
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Reid W, Pilitt K, Alford R, Cervantes-Medina A, Yu H, Aluvihare C, Harrell R, O'Brochta DA. An Anopheles stephensi Promoter-Trap: Augmenting Genome Annotation and Functional Genomics. G3 (BETHESDA, MD.) 2018; 8:3119-3130. [PMID: 30135106 PMCID: PMC6169391 DOI: 10.1534/g3.118.200347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022]
Abstract
The piggyBac transposon was modified to generate gene trap constructs, which were then incorporated into the genome of the Asian malaria vector, Anopheles stephensi and remobilized through genetic crosses using a piggyBac transposase expressing line. A total of 620 remobilization events were documented, and 73 were further characterized at the DNA level to identify patterns in insertion site preferences, remobilization frequencies, and remobilization patterns. Overall, the use of the tetameric AmCyan reporter as the fusion peptide displayed a preference for insertion into the 5'-end of transcripts. Notably 183 - 44882 bp upstream of the An. stephensi v1.0 ab initio gene models, which demonstrated that the promoter regions for the genes of An. stephensi are further upstream of the 5'-proximal regions of the genes in the ab inito models than may be otherwise predicted. RNA-Seq transcript coverage supported the insertion of the splice acceptor gene trap element into 5'-UTR introns for nearly half of all insertions identified. The use of a gene trap element that prefers insertion into the 5'-end of genes supports the use of this technology for the random generation of knock-out mutants, as well as the experimental confirmation of 5'-UTR introns in An. stephensi.
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Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Kristina Pilitt
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Robert Alford
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Adriana Cervantes-Medina
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Hao Yu
- Department of Plant Protection, Henan Institute of Science and Technology, East Street Huan-Lan, Xinxiang City, Henan Province 453003, CHINA
| | - Channa Aluvihare
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Rob Harrell
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
- Department of Entomology, University of Maryland College Park, 4112 Plant Sciences Building, College Park, MD 20742-4454
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12
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Chen J, Wu C, Zhang B, Cai Z, Wei L, Li Z, Li G, Guo T, Li Y, Guo W, Wang X. PiggyBac Transposon-Mediated Transgenesis in the Pacific Oyster ( Crassostrea gigas) - First Time in Mollusks. Front Physiol 2018; 9:811. [PMID: 30061837 PMCID: PMC6054966 DOI: 10.3389/fphys.2018.00811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/08/2018] [Indexed: 11/25/2022] Open
Abstract
As an effective method of transgenesis, the plasmid of PiggyBac transposon containing GFP (PiggyBac) transposon system has been widely used in various organisms but not yet in mollusks. In this work, piggyBac containing green fluorescent protein (GFP) was transferred into the Pacific oyster (Crassostrea gigas) by sperm-mediated gene transfer with or without electroporation. Fluorescent larvae were then observed and isolated under an inverted fluorescence microscope, and insertion of piggyBac was tested by polymerase chain reaction (PCR) using genomic DNA as template. Oyster larvae with green fluorescence were observed after transgenesis with or without electroporation, but electroporation increased the efficiency of sperm-mediated transgenesis. Subsequently, the recombinant piggyBac plasmid containing gGH (piggyBac-gGH) containing GFP and a growth hormone gene from orange-spotted grouper (gGH) was transferred into oysters using sperm mediation with electroporation, and fluorescent larvae were observed and isolated. The insertion of piggyBac-gGH was tested by PCR and genome walking analysis. PCR analysis indicated that piggyBac-gGH was transferred into oyster larvae; genome walking analysis further showed the detailed location where piggyBac-gGH was inserted in the oyster genome. This is the first time that piggyBac transposon-mediated transgenesis has been applied in mollusks.
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Affiliation(s)
- Jun Chen
- School of Agriculture, Ludong University, Yantai, China
| | - Changlu Wu
- School of Agriculture, Ludong University, Yantai, China
| | - Baolu Zhang
- Consultation Center, State Oceanic Administration, Beijing, China
| | - Zhongqiang Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Zhuang Li
- School of Agriculture, Ludong University, Yantai, China
| | - Guangbin Li
- School of Agriculture, Ludong University, Yantai, China
| | - Ting Guo
- School of Agriculture, Ludong University, Yantai, China
| | - Yongchuan Li
- School of Agriculture, Ludong University, Yantai, China
| | - Wen Guo
- Center for Mollusc Study and Development, Marine Biology Institute of Shandong Province, Qingdao, China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
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13
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Soga A, Ko‐ketsu M, Fukumoto S. Development of a
bsd
‐blasticidin selection system in
Plasmodium berghei. FEBS Lett 2018; 592:1847-1855. [DOI: 10.1002/1873-3468.13100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Akira Soga
- National Research Center for Protozoan Diseases Obihiro University of Agriculture and Veterinary Medicine Japan
| | - Mami Ko‐ketsu
- National Research Center for Protozoan Diseases Obihiro University of Agriculture and Veterinary Medicine Japan
| | - Shinya Fukumoto
- National Research Center for Protozoan Diseases Obihiro University of Agriculture and Veterinary Medicine Japan
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14
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Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E, Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig NL, Guittet E. Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase. Nucleic Acids Res 2018; 46:2660-2677. [PMID: 29385532 PMCID: PMC5861402 DOI: 10.1093/nar/gky044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 12/16/2022] Open
Abstract
The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5'-TGCGT-3'/3'-ACGCA-5' motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity.
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Affiliation(s)
- Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Silke A Wieninger
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Jennifer L Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julien Bischerour
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Séverine Moriau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Benjamin Bardiaux
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Nathalie Mathy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Mireille Bétermier
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Guittet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
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15
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Strobl F, Anderl A, Stelzer EHK. A universal vector concept for a direct genotyping of transgenic organisms and a systematic creation of homozygous lines. eLife 2018; 7:e31677. [PMID: 29543587 PMCID: PMC5854464 DOI: 10.7554/elife.31677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/29/2018] [Indexed: 12/25/2022] Open
Abstract
Diploid transgenic organisms are either hemi- or homozygous. Genetic assays are, therefore, required to identify the genotype. Our AGameOfClones vector concept uses two clearly distinguishable transformation markers embedded in interweaved, but incompatible Lox site pairs. Cre-mediated recombination leads to hemizygous individuals that carry only one marker. In the following generation, heterozygous descendants are identified by the presence of both markers and produce homozygous progeny that are selected by the lack of one marker. We prove our concept in Tribolium castaneum by systematically creating multiple functional homozygous transgenic lines suitable for long-term fluorescence live imaging. Our approach saves resources and simplifies transgenic organism handling. Since the concept relies on the universal Cre-Lox system, it is expected to work in all diploid model organisms, for example, insects, zebrafish, rodents and plants. With appropriate adaptions, it can be used in knock-out assays to preselect homozygous individuals and thus minimize the number of wasted animals.
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Affiliation(s)
- Frederic Strobl
- Physical Biology, BMLS, CEF-MCGoethe UniversitätFrankfurt am MainGermany
| | - Anita Anderl
- Physical Biology, BMLS, CEF-MCGoethe UniversitätFrankfurt am MainGermany
| | - Ernst HK Stelzer
- Physical Biology, BMLS, CEF-MCGoethe UniversitätFrankfurt am MainGermany
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16
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Laptev IA, Raevskaya NM, Filimonova NA, Sineoky SP. The piggyBac Transposon as a Tool in Genetic Engineering. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s000368381709006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Soga A, Bando H, Ko-Ketsu M, Masuda-Suganuma H, Kawazu SI, Fukumoto S. High efficacy in vitro selection procedure for generating transgenic parasites of Plasmodium berghei using an antibiotic toxic to rodent hosts. Sci Rep 2017. [PMID: 28638105 PMCID: PMC5479828 DOI: 10.1038/s41598-017-04244-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The malaria parasite Plasmodium berghei is one of the main rodent malaria models. A shortcoming of this model parasite is its low flexibility in genetic manipulation. As this parasite cannot be continuously propagated in cell cultures, in vivo drug selection procedures are necessary to isolate genetic mutants. Drugs harmful to rodents therefore cannot be used for drug selection, which restricts the range of genetic manipulation. In this study, we addressed this problem by establishing a novel in vitro culture drug selection method, which we used in combination with other established methods to successfully isolate genetically manipulated parasites. The target mutants were enriched to the desired level within two weeks. We show that our system can also be used for sequential genetic manipulation of parasites carrying the traditionally used selection markers, demonstrate the procedure’s versatility, and show its use in isolating specific genetically manipulated parasites. This novel in vitro selection method increases the number of available selection markers, allowing more extensive genetic manipulation in malaria parasite research.
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Affiliation(s)
- Akira Soga
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Hironori Bando
- Department of immunoparasitology, Research Institute for Microbial Disease, Osaka University, Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Mami Ko-Ketsu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Hirono Masuda-Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Shin-Ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Shinya Fukumoto
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan.
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18
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Bai DP, Yang MM, Qu L, Chen YL. Generation of a transgenic cashmere goat using the piggyBac transposition system. Theriogenology 2017; 93:1-6. [DOI: 10.1016/j.theriogenology.2017.01.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 01/04/2023]
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19
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The Functionality of Minimal PiggyBac Transposons in Mammalian Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e369. [PMID: 27701401 PMCID: PMC5095681 DOI: 10.1038/mtna.2016.76] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 07/12/2016] [Indexed: 12/11/2022]
Abstract
Minimal piggyBac vectors are a modified single-plasmid version of the classical piggyBac delivery system that can be used for stable transgene integration. These vectors have a truncated terminal domain in the delivery cassette and thus, integrate significantly less flanking transposon DNA into host cell chromatin than classical piggyBac vectors. Herein, we test various characteristics of this modified transposon. The integration efficiency of minimal piggyBac vectors was inversely related to the size of both the transposon and the entire plasmid, but inserts as large as 15 kb were efficiently integrated. Open and super-coiled vectors demonstrated the same integration efficiency while DNA methylation decreased the integration efficiency and silenced the expression of previously integrated sequences in some cell types. Importantly, the incidence of plasmid backbone integration was not increased above that seen in nontransposon control vectors. In BALB/c mice, we demonstrated prolonged expression of two transgenes (intracellular mCherry and secretable Gaussia luciferase) when delivered by the minimal piggyBac that resulted in a more sustained antibody production against the immunogenic luciferase than when delivered by a transient (nontransposon) vector plasmid. We conclude that minimal piggyBac vectors are an effective alternative to other integrative systems for stable DNA delivery in vitro and in vivo.
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20
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Riabinina O, Task D, Marr E, Lin CC, Alford R, O'Brochta DA, Potter CJ. Organization of olfactory centres in the malaria mosquito Anopheles gambiae. Nat Commun 2016; 7:13010. [PMID: 27694947 PMCID: PMC5063964 DOI: 10.1038/ncomms13010] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/25/2016] [Indexed: 02/01/2023] Open
Abstract
Mosquitoes are vectors for multiple infectious human diseases and use a variety of sensory cues (olfactory, temperature, humidity and visual) to locate a human host. A comprehensive understanding of the circuitry underlying sensory signalling in the mosquito brain is lacking. Here we used the Q-system of binary gene expression to develop transgenic lines of Anopheles gambiae in which olfactory receptor neurons expressing the odorant receptor co-receptor (Orco) gene are labelled with GFP. These neurons project from the antennae and maxillary palps to the antennal lobe (AL) and from the labella on the proboscis to the suboesophageal zone (SEZ), suggesting integration of olfactory and gustatory signals occurs in this brain region. We present detailed anatomical maps of olfactory innervations in the AL and the SEZ, identifying glomeruli that may respond to human body odours or carbon dioxide. Our results pave the way for anatomical and functional neurogenetic studies of sensory processing in mosquitoes.
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Affiliation(s)
- Olena Riabinina
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, 434 Rangos Building, Baltimore, Maryland 21205, USA
| | - Darya Task
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, 434 Rangos Building, Baltimore, Maryland 21205, USA
| | - Elizabeth Marr
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, 434 Rangos Building, Baltimore, Maryland 21205, USA
| | - Chun-Chieh Lin
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, 434 Rangos Building, Baltimore, Maryland 21205, USA
| | - Robert Alford
- University of Maryland College Park, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
| | - David A O'Brochta
- University of Maryland College Park, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
| | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, 434 Rangos Building, Baltimore, Maryland 21205, USA
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21
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Mishra P, Furey C, Balaraman V, Fraser MJ. Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes. Viruses 2016; 8:v8060163. [PMID: 27294950 PMCID: PMC4926183 DOI: 10.3390/v8060163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 12/18/2022] Open
Abstract
The chikungunya virus (CHIKV) is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates with the introduction of its major vector, Aedes albopictus. CHIKV causes a disease frequently misdiagnosed as dengue fever, with potentially life-threatening symptoms that can result in a longer-term debilitating arthritis. The increasing risk of spread from endemic regions via human travel and commerce and the current absence of a vaccine put a significant proportion of the world population at risk for this disease. In this study we designed and tested hammerhead ribozymes (hRzs) targeting CHIKV structural protein genes of the RNA genome as potential antivirals both at the cellular and in vivo level. We employed the CHIKV strain 181/25, which exhibits similar infectivity rates in both Vero cell cultures and mosquitoes. Virus suppression assay performed on transformed Vero cell clones of all seven hRzs demonstrated that all are effective at inhibiting CHIKV in Vero cells, with hRz #9 and #14 being the most effective. piggyBac transformation vectors were constructed using the Ae. aegypti t-RNAval Pol III promoted hRz #9 and #14 effector genes to establish a total of nine unique transgenic Higgs White Eye (HWE) Ae. aegypti lines. Following confirmation of transgene expression by real-time polymerase chain reaction (RT-PCR), comparative TCID50-IFA analysis, in situ Immuno-fluorescent Assays (IFA) and analysis of salivary CHIKV titers demonstrated effective suppression of virus replication at 7 dpi in heterozygous females of each of these transgenic lines compared with control HWE mosquitoes. This report provides a proof that appropriately engineered hRzs are powerful antiviral effector genes suitable for population replacement strategies
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Affiliation(s)
- Priya Mishra
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, P.O. Box 369, Notre Dame, IN 46556, USA.
| | - Colleen Furey
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, P.O. Box 369, Notre Dame, IN 46556, USA.
| | - Velmurugan Balaraman
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, P.O. Box 369, Notre Dame, IN 46556, USA.
| | - Malcolm J Fraser
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, P.O. Box 369, Notre Dame, IN 46556, USA.
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22
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Abstract
The piggyBac transposon was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and dissimilarity to the other DNA transposon families, the piggyBac transposon was not recognized as a member of a large transposon superfamily for a long time. Initially, the piggyBac transposon was thought to be a rare transposon. This view, however, has now been completely revised as a number of fully sequenced genomes have revealed the presence of piggyBac-like repetitive elements. The isolation of active copies of the piggyBac-like elements from several distinct species further supported this revision. This includes the first isolation of an active mammalian DNA transposon identified in the bat genome. To date, the piggyBac transposon has been deeply characterized and it represents a number of unique characteristics. In general, all members of the piggyBac superfamily use TTAA as their integration target sites. In addition, the piggyBac transposon shows precise excision, i.e., restoring the sequence to its preintegration state, and can transpose in a variety of organisms such as yeasts, malaria parasites, insects, mammals, and even in plants. Biochemical analysis of the chemical steps of transposition revealed that piggyBac does not require DNA synthesis during the actual transposition event. The broad host range has attracted researchers from many different fields, and the piggyBac transposon is currently the most widely used transposon system for genetic manipulations.
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23
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Loperfido M, Jarmin S, Dastidar S, Di Matteo M, Perini I, Moore M, Nair N, Samara-Kuko E, Athanasopoulos T, Tedesco FS, Dickson G, Sampaolesi M, VandenDriessche T, Chuah MK. piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts. Nucleic Acids Res 2015; 44:744-60. [PMID: 26682797 PMCID: PMC4737162 DOI: 10.1093/nar/gkv1464] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/28/2015] [Indexed: 01/02/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes.
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Affiliation(s)
- Mariana Loperfido
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Susan Jarmin
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Sumitava Dastidar
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium
| | - Mario Di Matteo
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Ilaria Perini
- Translational Cardiomyology Laboratory, Embryo and Stem Cell Biology Unit, Department of Development and Regeneration, University of Leuven, Leuven 3000, Belgium
| | - Marc Moore
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Nisha Nair
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium
| | - Ermira Samara-Kuko
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium
| | - Takis Athanasopoulos
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK Faculty of Science & Engineering, University of Wolverhampton, Wolverhampton, WV1 1LY, UK
| | | | - George Dickson
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Maurilio Sampaolesi
- Translational Cardiomyology Laboratory, Embryo and Stem Cell Biology Unit, Department of Development and Regeneration, University of Leuven, Leuven 3000, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Marinee K Chuah
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
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TAL effectors mediate high-efficiency transposition of the piggyBac transposon in silkworm Bombyx mori L. Sci Rep 2015; 5:17172. [PMID: 26608076 PMCID: PMC4660427 DOI: 10.1038/srep17172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 10/26/2015] [Indexed: 12/19/2022] Open
Abstract
The piggyBac (PB) transposon is one of the most useful transposable
elements, and has been successfully used for genetic manipulation in more than a
dozen species. However, the efficiency of PB-mediated transposition is still
insufficient for many purposes. Here, we present a strategy to enhance transposition
efficiency using a fusion of transcription activator-like effector (TALE) and the
PB transposase (PBase). The results demonstrate that the
TALE-PBase fusion protein which is engineered in this study can produce a
significantly improved stable transposition efficiency of up to 63.9%, which is at
least 7 times higher than the current transposition efficiency in silkworm.
Moreover, the average number of transgene-positive individuals increased up to
5.7-fold, with each positive brood containing an average of 18.1 transgenic
silkworms. Finally, we demonstrate that TALE-PBase fusion-mediated
PB transposition presents a new insertional preference compared with
original insertional preference. This method shows a great potential and value for
insertional therapy of many genetic diseases. In conclusion, this new and powerful
transposition technology will efficiently promote genetic manipulation studies in
both invertebrates and vertebrates.
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An efficient strategy for producing a stable, replaceable, highly efficient transgene expression system in silkworm, Bombyx mori. Sci Rep 2015; 5:8802. [PMID: 25739894 DOI: 10.1038/srep08802] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/04/2015] [Indexed: 12/16/2022] Open
Abstract
We developed an efficient strategy that combines a method for the post-integration elimination of all transposon sequences, a site-specific recombination system, and an optimized fibroin H-chain expression system to produce a stable, replaceable, highly efficient transgene expression system in the silkworm (Bombyx mori) that overcomes the disadvantages of random insertion and post-integration instability of transposons. Here, we generated four different transgenic silkworm strains, and of one the transgenic strains, designated TS1-RgG2, with up to 16% (w/w) of the target protein in the cocoons, was selected. The subsequent elimination of all the transposon sequences from TS1-RgG2 was completed by the heat-shock-induced expression of the transposase in vivo. The resulting transgenic silkworm strain was designated TS3-g2 and contained only the attP-flanked optimized fibroin H-chain expression cassette in its genome. A phiC31/att-system-based recombinase-mediated cassette exchange (RMCE) method could be used to integrate other genes of interest into the same genome locus between the attP sites in TS3-g2. Controlling for position effects with phiC31-mediated RMCE will also allow the optimization of exogenous protein expression and fine gene function analyses in the silkworm. The strategy developed here is also applicable to other lepidopteran insects, to improve the ecological safety of transgenic strains in biocontrol programs.
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26
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Heterelogous expression of mutated HLA-G decreases immunogenicity of human embryonic stem cells and their epidermal derivatives. Stem Cell Res 2014; 13:342-54. [PMID: 25218797 DOI: 10.1016/j.scr.2014.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/29/2014] [Accepted: 08/08/2014] [Indexed: 12/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) are capable of extensive self-renewal and expansion and can differentiate into any somatic tissue, making them useful for regenerative medicine applications. Allogeneic transplantation of hESC-derived tissues from results in immunological rejection absent adjunctive immunosuppression. The goal of our study was to generate a universal pluripotent stem cell source by nucleofecting a mutated human leukocyte antigen G (mHLA-G) gene into hESCs using the PiggyBac transposon. We successfully generated stable mHLA-G(EF1α)-hESC lines using chEF1α promoter system that stably expressed mHLA-G protein during prolonged undifferentiated proliferation andin differentiated embryoid bodies as well as teratomas. Morphology, karyotype, and telomerase activity of mHLA-G expressing hESC were normal. Immunofluorescence staining and flow cytometry analysis revealed persistent expression of pluripotent markers, OCT-3/4 and SSEA-4, in undifferentiated mHLA-G(EF1α)-hESC. Nucleofected hESC formed teratomas and when directed to differentiate into epidermal precursors, expressed high levels of mHLA-G and keratinocyte markers K14 and CD29. Natural killer cell cytotoxicity assays demonstrated a significant decrease in lysis of mHLA-G(EF1a)-hESC targets relative to control cells. Similar results were obtained with mHLA-G(EF1α)-hESC-derived epidermal progenitors (hEEP). One way mixed T lymphocyte reactions unveiled that mHLA-G(EF1a)-hESC and -hEEP restrained the proliferative activity of mixed T lymphocytes. We conclude that heterologous expression of mHLA-G decreases immunogenicity of hESCs and their epidermal differentiated derivatives.
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Di Matteo M, Samara-Kuko E, Ward NJ, Waddington SN, Waddingon SN, McVey JH, Chuah MKL, VandenDriessche T. Hyperactive piggyBac transposons for sustained and robust liver-targeted gene therapy. Mol Ther 2014; 22:1614-24. [PMID: 25034357 PMCID: PMC4435487 DOI: 10.1038/mt.2014.131] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/27/2014] [Indexed: 01/14/2023] Open
Abstract
The development of robust nonviral vectors could facilitate clinical gene therapy applications and may overcome some of the immune complications of viral vectors. Nevertheless, most nonviral gene deliver approaches typically yield only transient and/or low gene expression. To address these caveats, we have explored piggyBac transposons to correct hemophilia B by liver-directed factor IX (FIX) gene therapy in hemophilic mice. To achieve this, we combined the use of: (i) a hyperactive codon-optimized piggyBac transposase, (ii) a computationally enhanced liver-specific promoter, (iii) a hyperfunctional codon-optimized FIX transgene (FIX R338L Padua), and (iv) a modification of the transposon terminal repeats. This combination strategy resulted in a robust 400-fold improvement in vector performance in hepatocytes, yielding stable supraphysiologic human FIX activity (>1 year). Liver-specific expression resulted in the induction of FIX-specific immune tolerance. Remarkably, only very low transposon/transposase doses were required to cure the bleeding diathesis. Similarly, PB transposons could be used to express supraphysiologic factor VIII levels using low transposon/transposase doses. PB transposition did not induce tumors in a sensitive hepatocellular carcinoma-prone mouse model. These results underscore the potency and relative safety of the latest generation PB transposons, which constitutes a versatile platform for stable and robust secretion of therapeutic proteins.
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Affiliation(s)
- Mario Di Matteo
- 1] Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium [2] Center for Molecular and Vascular Biology, Department of Cardiovascular Medicine, University of Leuven, Leuven, Belgium
| | - Emira Samara-Kuko
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium
| | - Natalie J Ward
- Molecular Immunology Unit, Institute of Child Health, University College London, London, UK
| | - Simon N Waddington
- 1] Institute for Women's Health Gene Transfer Technology Group, University College London, London, UK [2] School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa
| | | | - John H McVey
- University of Surrey, Molecular Medicine Group, Surrey, UK
| | - Marinee K L Chuah
- 1] Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium [2] Center for Molecular and Vascular Biology, Department of Cardiovascular Medicine, University of Leuven, Leuven, Belgium
| | - Thierry VandenDriessche
- 1] Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium [2] Center for Molecular and Vascular Biology, Department of Cardiovascular Medicine, University of Leuven, Leuven, Belgium
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Hu K. All roads lead to induced pluripotent stem cells: the technologies of iPSC generation. Stem Cells Dev 2014; 23:1285-300. [PMID: 24524728 PMCID: PMC4046204 DOI: 10.1089/scd.2013.0620] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/12/2014] [Indexed: 12/26/2022] Open
Abstract
Generation of induced pluripotent stem cells (iPSCs) via the ectopic expression of reprogramming factors is a simple, advanced, yet often perplexing technology due to low efficiency, slow kinetics, and the use of numerous distinct systems for factor delivery. Scientists have used almost all available approaches for the delivery of reprogramming factors. Even the well-established retroviral vectors confuse some scientists due to different tropisms in use. The canonical virus-based reprogramming poses many problems, including insertional mutagenesis, residual expression and re-activation of reprogramming factors, uncontrolled silencing of transgenes, apoptosis, cell senescence, and strong immunogenicity. To eliminate or alleviate these problems, scientists have tried various other approaches for factor delivery and transgene removal. These include transient transfection, nonintegrating viral vectors, Cre-loxP excision of transgenes, excisable transposon, protein transduction, RNA transfection, microRNA transfection, RNA virion, RNA replicon, nonintegrating replicating episomal plasmids, minicircles, polycistron, and preintegration of inducible reprogramming factors. These alternative approaches have their own limitations. Even iPSCs generated with RNA approaches should be screened for possible transgene insertions mediated by active endogenous retroviruses in the human genome. Even experienced researchers may encounter difficulty in selecting and using these different technologies. This survey presents overviews of iPSC technologies with the intention to provide a quick yet comprehensive reference for both new and experienced reprogrammers.
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Affiliation(s)
- Kejin Hu
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Insitute, School of Medicine, University of Alabama at Birmingham , Birmingham, Alabama
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29
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Hu K. Vectorology and factor delivery in induced pluripotent stem cell reprogramming. Stem Cells Dev 2014; 23:1301-15. [PMID: 24625220 PMCID: PMC4046209 DOI: 10.1089/scd.2013.0621] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/13/2014] [Indexed: 12/26/2022] Open
Abstract
Induced pluripotent stem cell (iPSC) reprogramming requires sustained expression of multiple reprogramming factors for a limited period of time (10-30 days). Conventional iPSC reprogramming was achieved using lentiviral or simple retroviral vectors. Retroviral reprogramming has flaws of insertional mutagenesis, uncontrolled silencing, residual expression and re-activation of transgenes, and immunogenicity. To overcome these issues, various technologies were explored, including adenoviral vectors, protein transduction, RNA transfection, minicircle DNA, excisable PiggyBac (PB) transposon, Cre-lox excision system, negative-sense RNA replicon, positive-sense RNA replicon, Epstein-Barr virus-based episomal plasmids, and repeated transfections of plasmids. This review provides summaries of the main vectorologies and factor delivery systems used in current reprogramming protocols.
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Affiliation(s)
- Kejin Hu
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, School of Medicine, University of Alabama at Birmingham , Birmingham, Alabama
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A modified piggybac transposon system mediated by exogenous mRNA to perform gene delivery in bovine mammary epithelial cells. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0811-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Solodushko V, Bitko V, Fouty B. Minimal piggyBac vectors for chromatin integration. Gene Ther 2013; 21:1-9. [PMID: 24131979 DOI: 10.1038/gt.2013.52] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/16/2013] [Accepted: 08/27/2013] [Indexed: 01/22/2023]
Abstract
We describe novel transposon piggyBac vectors engineered to deliver transgenes as efficiently as currently available piggyBac systems, but with significantly less helper DNA co-delivered into the host genome. To generate these plasmids, we identified a previously unreported aspect of transposon biology, that the full-length terminal domains required for successful plasmid-to-chromatin transgene delivery can be removed from the transgene delivery cassette to other parts of the plasmid without significantly impairing transposition efficiency. This is achieved by including in the same plasmid, an additional helper piggyBac sequence that contains both long terminal domains, but is modified to prevent its transposition into the host genome. This design decreases the size of the required terminal domains within the delivered gene cassette of the piggyBac vector from about 1500 to just 98 base pairs. By removing these sequences from the delivered gene cassette, they are no longer incorporated into the host genome which may reduce the risk of target cell transformation.
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Affiliation(s)
- V Solodushko
- 1] Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, USA [2] Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, USA
| | - V Bitko
- NanoBio Corporation, Ann Arbor, MI, USA
| | - B Fouty
- 1] Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, USA [2] Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, USA [3] Department of Internal Medicine University of South Alabama School of Medicine, Mobile, AL, USA
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32
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Menke DB. Engineering subtle targeted mutations into the mouse genome. Genesis 2013; 51:605-18. [PMID: 23913666 DOI: 10.1002/dvg.22422] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 07/25/2013] [Accepted: 07/26/2013] [Indexed: 12/13/2022]
Abstract
Homologous recombination in embryonic stem (ES) cells offers an exquisitely precise mechanism to introduce targeted modifications to the mouse genome. This ability to produce specific alterations to the mouse genome has become an essential tool for the analysis of gene function and the development of mouse models of human disease. Of the many thousands of mouse alleles that have been generated by gene targeting, the majority are designed to completely ablate gene function, to create conditional alleles that are inactivated in the presence of Cre recombinase, or to produce reporter alleles that label-specific tissues or cell populations (Eppig et al., 2012, Nucleic Acids Res 40:D881-D886). However, there is a variety of powerful motivations for the introduction of subtle targeted mutations (STMs) such as point mutations, small deletions, or small insertions into the mouse genome. The introduction of STMs allows the ablation of specific transcript isoforms, permits the functional investigation of particular domains or amino acids within a protein, provides the ability to study the role of specific sites with in cis-regulatory elements, and can result in better mouse models of human genetic disorders. In this review, I examine the current strategies that are commonly used to introduce STMs into the mouse genome and highlight new gene targeting technologies, including TALENs and CRISPR/Cas, which are likely to influence the future of gene targeting in mice.
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Affiliation(s)
- Douglas B Menke
- Department of Genetics, University of Georgia, Athens, Georgia
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PK-15 cells transfected with porcine CD163 by PiggyBac transposon system are susceptible to porcine reproductive and respiratory syndrome virus. J Virol Methods 2013; 193:383-90. [PMID: 23835031 DOI: 10.1016/j.jviromet.2013.06.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/18/2013] [Accepted: 06/26/2013] [Indexed: 01/12/2023]
Abstract
The PiggyBac (PB) transposon system is a non-viral DNA-transfer system in which a transposase directs integration of a PB transposon into a TTAA site in the genome. Transgenic expression of porcine CD163 is necessary and sufficient to confer non-permissive cells susceptible to infection with porcine reproductive and respiratory syndrome virus (PRRSV). Such permissive cells can be used as a tool for PRRSV cellular receptor and other studies. One of the problems in studying PRRSV is the lack of porcine cell lines. In this study, efficient transfection and expression of porcine CD163 in PK-15 cells by PB transposition was demonstrated. The stable PK-15CD163 cell line was used in PRRSV infection assays. The data indicated that the average PB transgene copy number per genome was approximately 10. In line with previous literature the integration of PB into the genome had a bias toward the TTAA chromosomal site. The PK-15CD163 cell line was susceptible to infection by different PRRSV strains and the virus grew to similar titers compared to the Marc-145 cell line. This simplification of PK-15CD163 cell line production will provide a valuable tool to facilitate PRRSV cellular receptor studies and to accelerate existing vectors for PK-15 cell-based gene transfer and expression.
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Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning. Nature 2013; 497:628-32. [PMID: 23624372 PMCID: PMC4197975 DOI: 10.1038/nature12157] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 04/08/2013] [Indexed: 12/20/2022]
Abstract
The ability of signaling proteins to traverse tissues containing tightly packed cells is of fundamental importance for cell specification and tissue development, however, how this is achieved at a cellular level remains poorly understood1. For over a century, the vertebrate limb bud has served as a paradigm to study cell signaling during embryonic development2. Here we optimize single cell real-time imaging to delineate the cellular mechanisms for how signaling proteins, such as Sonic Hedgehog (Shh), that possess membrane-bound covalent lipid modifications transverse long distances within the limb bud in vivo. By directly imaging Shh ligand production under native regulatory control, our findings show that Shh is unexpectedly produced in the form of a particle that remains associated with the cell via long cytoplasmic extensions that span several cell diameters. We show that these cellular extensions are a specialized class of actin-based filopodia with novel cytoskeletal features that have not been previously described. Strikingly, particles containing Shh traffic along these extensions with a net anterograde movement within the field of Shh cell signaling. We further show that in Shh responding cells specific subsets of Shh co-receptors, including Cdo and Boc, actively distribute and co-localize in specific micro-domains within filopodial extensions, far from the cell body. Stabilized interactions are formed between filopodia containing Shh ligand and those containing co-receptors over a long-range. These results suggest that contact-mediated release propagated by specialized filopodia contributes to the delivery of Shh at a distance. Together, these studies identify an important mode of communication between cells that significantly extends our understanding of ligand movement and reception during vertebrate tissue patterning.
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Di Matteo M, Belay E, Chuah MK, Vandendriessche T. Recent developments in transposon-mediated gene therapy. Expert Opin Biol Ther 2012; 12:841-58. [PMID: 22679910 DOI: 10.1517/14712598.2012.684875] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The continuous improvement of gene transfer technologies has broad implications for stem cell biology, gene discovery, and gene therapy. Although viral vectors are efficient gene delivery vehicles, their safety, immunogenicity and manufacturing challenges hamper clinical progress. In contrast, non-viral gene delivery systems are less immunogenic and easier to manufacture. AREAS COVERED In this review, we explore the emerging potential of transposons in gene and cell therapy. The safety, efficiency, and biology of novel hyperactive Sleeping Beauty (SB) and piggyBac (PB) transposon systems will be highlighted for ex vivo gene therapy in clinically relevant adult stem/progenitor cells, particularly hematopoietic stem cells (HSCs), mesenchymal stem cells (MSCs), myoblasts, and induced pluripotent stem (iPS) cells. Moreover, efforts toward in vivo transposon-based gene therapy will be discussed. EXPERT OPINION The latest generation SB and PB transposons currently represent some of the most attractive systems for stable non-viral genetic modification of primary cells, particularly adult stem cells. This paves the way toward the use of transposons as a non-viral gene therapy approach to correct hereditary disorders including those that affect the hematopoietic system. The development of targeted integration into "safe harbor" genetic loci may further improve their safety profile.
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Affiliation(s)
- Mario Di Matteo
- Free University of Brussels, Division of Gene Therapy & Regenerative Medicine, Laarbeeklaan 103, B-1090 Brussels, Belgium
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Gal4-based enhancer-trapping in the malaria mosquito Anopheles stephensi. G3-GENES GENOMES GENETICS 2012; 2:1305-15. [PMID: 23173082 PMCID: PMC3484661 DOI: 10.1534/g3.112.003582] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/22/2012] [Indexed: 12/16/2022]
Abstract
Transposon-based forward and reverse genetic technologies will contribute greatly to ongoing efforts to study mosquito functional genomics. A piggyBac transposon-based enhancer-trap system was developed that functions efficiently in the human malaria vector, Anopheles stephensi. The system consists of six transgenic lines of Anopheles stephensi, each with a single piggyBac-Gal4 element in a unique genomic location; six lines with a single piggyBac-UAStdTomato element; and two lines, each with a single Minos element containing the piggyBac-transposase gene under the regulatory control of the hsp70 promoter from Drosophila melanogaster. Enhancer detection depended upon the efficient remobilization of piggyBac-Gal4 transposons, which contain the yeast transcription factor gene Gal4 under the regulatory control of a basal promoter. Gal4 expression was detected through the expression of the fluorescent protein gene tdTomato under the regulatory control of a promoter with Gal4-binding UAS elements. From five genetic screens for larval- and adult-specific enhancers, 314 progeny were recovered from 24,250 total progeny (1.3%) with unique patterns of tdTomato expression arising from the influence of an enhancer. The frequency of piggyBac remobilization and enhancer detection was 2.5- to 3-fold higher in female germ lines compared with male germ lines. A small collection of enhancer-trap lines are described in which Gal4 expression occurred in adult female salivary glands, midgut, and fat body, either singly or in combination. These three tissues play critical roles during the infection of Anopheles stephensi by malaria-causing Plasmodium parasites. This system and the lines generated using it will be valuable resources to ongoing mosquito functional genomics efforts.
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Sharma N, Hollensen AK, Bak RO, Staunstrup NH, Schrøder LD, Mikkelsen JG. The impact of cHS4 insulators on DNA transposon vector mobilization and silencing in retinal pigment epithelium cells. PLoS One 2012; 7:e48421. [PMID: 23110238 PMCID: PMC3482222 DOI: 10.1371/journal.pone.0048421] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/25/2012] [Indexed: 12/29/2022] Open
Abstract
DNA transposons have become important vectors for efficient non-viral integration of transgenes into genomic DNA. The Sleeping Beauty (SB), piggyBac (PB), and Tol2 transposable elements have distinct biological properties and currently represent the most promising transposon systems for animal transgenesis and gene therapy. A potential obstacle, however, for persistent function of integrating vectors is transcriptional repression of the element and its genetic cargo. In this study we analyze the insulating effect of the 1.2-kb 5'-HS4 chicken β-globin (cHS4) insulator element in the context of SB, PB, and Tol2 transposon vectors. By examining transgene expression from genomically inserted transposon vectors encoding a marker gene driven by a silencing-prone promoter, we detect variable levels of transcriptional silencing for the three transposon systems in retinal pigment epithelium cells. Notably, the PB system seems less vulnerable to silencing. Incorporation of cHS4 insulator sequences into the transposon vectors results in 2.2-fold and 1.5-fold increased transgene expression levels for insulated SB and PB vectors, respectively, but an improved persistency of expression was not obtained for insulated transgenes. Colony formation assays and quantitative excision assays unveil enhanced SB transposition efficiencies by the inclusion of the cHS4 element, resulting in a significant increase in the stable transfection rate for insulated SB transposon vectors in human cell lines. Our findings reveal a positive impact of cHS4 insulator inclusion for SB and PB vectors in terms of increased transgene expression levels and improved SB stable transfection rates, but also the lack of a long-term protective effect of the cHS4 insulator against progressive transgene silencing in retinal pigment epithelium cells.
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Affiliation(s)
- Nynne Sharma
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Rasmus O. Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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Shao H, Li X, Nolan TJ, Massey HC, Pearce EJ, Lok JB. Transposon-mediated chromosomal integration of transgenes in the parasitic nematode Strongyloides ratti and establishment of stable transgenic lines. PLoS Pathog 2012; 8:e1002871. [PMID: 22912584 PMCID: PMC3415448 DOI: 10.1371/journal.ppat.1002871] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 07/06/2012] [Indexed: 11/28/2022] Open
Abstract
Genetic transformation is a potential tool for analyzing gene function and thereby identifying new drug and vaccine targets in parasitic nematodes, which adversely affect more than one billion people. We have previously developed a robust system for transgenesis in Strongyloides spp. using gonadal microinjection for gene transfer. In this system, transgenes are expressed in promoter-regulated fashion in the F1 but are silenced in subsequent generations, presumably because of their location in repetitive episomal arrays. To counteract this silencing, we explored transposon-mediated chromosomal integration of transgenes in S. ratti. To this end, we constructed a donor vector encoding green fluorescent protein (GFP) under the control of the Ss-act-2 promoter with flanking inverted tandem repeats specific for the piggyBac transposon. In three experiments, free-living Strongyloides ratti females were transformed with this donor vector and a helper plasmid encoding the piggyBac transposase. A mean of 7.9% of F1 larvae were GFP-positive. We inoculated rats with GFP-positive F1 infective larvae, and 0.5% of 6014 F2 individuals resulting from this host passage were GFP-positive. We cultured GFP-positive F2 individuals to produce GFP-positive F3 L3i for additional rounds of host and culture passage. Mean GFP expression frequencies in subsequent generations were 15.6% in the F3, 99.0% in the F4, 82.4% in the F5 and 98.7% in the F6. The resulting transgenic lines now have virtually uniform GFP expression among all progeny after at least 10 generations of passage. Chromosomal integration of the reporter transgenes was confirmed by Southern blotting and splinkerette PCR, which revealed the transgene flanked by S. ratti genomic sequences corresponding to five discrete integration sites. BLAST searches of flanking sequences against the S. ratti genome revealed integrations in five contigs. This result provides the basis for two powerful functional genomic tools in S. ratti: heritable transgenesis and insertional mutagenesis.
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Affiliation(s)
- Hongguang Shao
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Xinshe Li
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas J. Nolan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Holman C. Massey
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Edward J. Pearce
- Department of Pathology and Immunology, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - James B. Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Rostovskaya M, Fu J, Obst M, Baer I, Weidlich S, Wang H, Smith AJH, Anastassiadis K, Stewart AF. Transposon-mediated BAC transgenesis in human ES cells. Nucleic Acids Res 2012; 40:e150. [PMID: 22753106 PMCID: PMC3479164 DOI: 10.1093/nar/gks643] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transgenesis is a cornerstone of molecular biology. The ability to integrate a specifically engineered piece of DNA into the genome of a living system is fundamental to our efforts to understand life and exploit its implications for medicine, nanotechnology and bioprospecting. However, transgenesis has been hampered by position effects and multi-copy integration problems, which are mainly due to the use of small, plasmid-based transgenes. Large transgenes based on native genomic regions cloned into bacterial artificial chromosomes (BACs) circumvent these problems but are prone to fragmentation. Herein, we report that contrary to widely held notions, large BAC-sized constructs do not prohibit transposition. We also report the first reliable method for BAC transgenesis in human embryonic stem cells (hESCs). The PiggyBac or Sleeping Beauty transposon inverted repeats were integrated into BAC vectors by recombineering, followed by co-lipofection with the corresponding transposase in hESCs to generate robust fluorescent protein reporter lines for OCT4, NANOG, GATA4 and PAX6. BAC transposition delivers several advantages, including increased frequencies of single-copy, full-length integration, which will be useful in all transgenic systems but especially in difficult venues like hESCs.
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Affiliation(s)
- Maria Rostovskaya
- Stem Cell Engineering, BioInnovationsZentrum, Technische Universitaet Dresden, Dresden 01307, Germany
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Su H, Liu X, Yan W, Shi T, Zhao X, Blake DP, Tomley FM, Suo X. piggyBac transposon-mediated transgenesis in the apicomplexan parasite Eimeria tenella. PLoS One 2012; 7:e40075. [PMID: 22768223 PMCID: PMC3386905 DOI: 10.1371/journal.pone.0040075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 06/05/2012] [Indexed: 01/24/2023] Open
Abstract
piggyBac, a type II transposon that is useful for efficient transgenesis and insertional mutagenesis, has been used for effective and stable transfection in a wide variety of organisms. In this study we investigate the potential use of the piggyBac transposon system for forward genetics studies in the apicomplexan parasite Eimeria tenella. Using the restriction enzyme-mediated integration (REMI) method, E. tenella sporozoites were electroporated with a donor plasmid containing the enhanced yellow fluorescent protein (EYFP) gene flanked by piggyBac inverted terminal repeats (ITRs), an Asc I-linearized helper plasmid containing the transposase gene and the restriction enzyme Asc I. Subsequently, electroporated sporozoites were inoculated into chickens via the cloacal route and transfected progeny oocysts expressing EYFP were sorted by flow cytometry. A transgenic E. tenella population was selected by successive in vivo passage. Southern-blotting analysis showed that exogenous DNA containing the EYFP gene was integrated into the parasite genome at a limited number of integration sites and that the inserted part of the donor plasmid was the fragment located between the 5′ and 3′ ITRs as indicated by primer-specific PCR screening. Genome walking revealed that the insertion sites were TTAA-specific, which is consistent with the transposition characteristics of piggyBac.
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Affiliation(s)
- Huali Su
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xianyong Liu
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenchao Yan
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Tuanyuan Shi
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xinxin Zhao
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Damer P. Blake
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- Royal Veterinary College, Pathology and Infectious Diseases, North Mymms, Hertfordshire, United Kingdom
| | - Fiona M. Tomley
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- Royal Veterinary College, Pathology and Infectious Diseases, North Mymms, Hertfordshire, United Kingdom
| | - Xun Suo
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail:
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Pöyhönen M, de Vanssay A, Delmarre V, Hermant C, Todeschini AL, Teysset L, Ronsseray S. Homology-dependent silencing by an exogenous sequence in the Drosophila germline. G3 (BETHESDA, MD.) 2012; 2:331-8. [PMID: 22413086 PMCID: PMC3291502 DOI: 10.1534/g3.111.001925] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/24/2011] [Indexed: 11/25/2022]
Abstract
The study of P transposable element repression in Drosophila melanogaster led to the discovery of the trans-silencing effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences) represses in trans, in the female germline, a homologous P-lacZ transgene inserted in euchromatin. TSE shows variegation in ovaries and displays a maternal effect as well as epigenetic transmission through meiosis. In addition, TSE is highly sensitive to mutations affecting heterochromatin components (including HP1) and the Piwi-interacting RNA silencing pathway (piRNA), a homology-dependent silencing mechanism that functions in the germline. TSE appears thus to involve the piRNA-based silencing proposed to play a major role in P repression. Under this hypothesis, TSE may also be established when homology between the telomeric and target loci involves sequences other than P elements, including sequences exogenous to the D. melanogaster genome. We have tested whether TSE can be induced via lacZ sequence homology. We generated a piggyBac-otu-lacZ transgene in which lacZ is under the control of the germline ovarian tumor promoter, resulting in strong expression in nurse cells and the oocyte. We show that all piggyBac-otu-lacZ transgene insertions are strongly repressed by maternally inherited telomeric P-lacZ transgenes. This repression shows variegation between egg chambers when it is incomplete and presents a maternal effect, two of the signatures of TSE. Finally, this repression is sensitive to mutations affecting aubergine, a key player of the piRNA pathway. These data show that TSE can occur when silencer and target loci share solely a sequence exogenous to the D. melanogaster genome. This functionally supports the hypothesis that TSE represents a general repression mechanism which can be co-opted by new transposable elements to regulate their activity after a transfer to the D. melanogaster genome.
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Affiliation(s)
| | | | - Valérie Delmarre
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
| | - Catherine Hermant
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
| | | | - Laure Teysset
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
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Duvoisin R, Ayuk MA, Rinaldi G, Suttiprapa S, Mann VH, Lee CM, Harris N, Brindley PJ. Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells. Transgenic Res 2011; 21:511-21. [PMID: 21953124 DOI: 10.1007/s11248-011-9548-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 08/23/2011] [Indexed: 10/17/2022]
Abstract
Blood flukes or schistosomes are the causative agents of human schistosomiasis, one of the major neglected tropical diseases. Draft genome sequences have been reported for schistosomes, but functional genomics tools are needed to investigate the role and essentiality of the newly reported genes. Vector based RNA interference can contribute to functional genomics analysis for schistosomes. Using mRNA encoding reporter firefly luciferase as a model target, we compared the performance of a schistosome and a human promoter from the U6 gene in driving shRNA in human fibrosarcoma cells and in cultured schistosomes. Further, both a retroviral [Murine leukemia virus (MLV)] and plasmid (piggyBac, pXL-Bac II) vector were utilized. The schistosome U6 gene promoter was 270 bp in length, the human U6 gene promoter was 264 bp; they shared 41% identity. Following transduction of both HT1080 fibrosarcoma cells and schistosomules of Schistosoma mansoni with pseudotyped MLV virions, stronger knockdown of luciferase activity was seen with the virions encoding the human U6 promoter driven shRNA than the schistosome U6 promoter. A similar trend was seen after transfection of HT1080 cells and schistosomules with the pXL-Bac-II constructs-stronger knockdown of luciferase activity was seen with constructs encoding the human compared to schistosome U6 promoter. The findings indicate that a human U6 gene promoter drives stronger shRNA activity than its schistosome orthologue, not only in a human cancer cell line but also in larval schistosomes. This RNA polymerase III promoter represents a potentially valuable component for vector based RNA interference studies in schistosomes and related platyhelminth parasites.
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Affiliation(s)
- Raphaël Duvoisin
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University Medical Center, Ross Hall 448, 2300 I Street NW, Washington, DC 20037, USA
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piggyBac transposon remobilization and enhancer detection in Anopheles mosquitoes. Proc Natl Acad Sci U S A 2011; 108:16339-44. [PMID: 21930941 DOI: 10.1073/pnas.1110628108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Technical advances in mosquito biology are enabling the development of new approaches to vector control. Absent are powerful forward-genetics technologies, such as enhancer and gene traps, that permit determination of gene functions from the phenotypes arising from transposon insertion mutations. We show that the piggyBac transposon is highly active in the germline of the human malaria vector Anopheles stephensi. Up to 6% of the progeny from transgenic A. stephensi containing a single 6-kb piggyBac element with a marker gene expressing EGFP had the vector in new genomic locations when piggyBac transposase was provided in trans from a second integrated transgene. The active transposition of piggyBac resulted in the efficient detection of enhancers, with ~10% of the progeny with piggyBac in new locations with novel patterns of EGFP expression in third and fourth instar larvae and in adults. The availability of advanced transgenic capabilities such as efficient transposon-based forward-genetics technologies for Anopheles mosquitoes not only will accelerate our understanding of mosquito functional genomics and the development of novel vector and disease transmission control strategies, but also will enable studies by evolutionary developmental biologists, virologists, and parasitologists.
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Kahlon AS, Hice RH, O'Brochta DA, Atkinson PW. DNA binding activities of the Herves transposase from the mosquito Anopheles gambiae. Mob DNA 2011; 2:9. [PMID: 21689391 PMCID: PMC3143072 DOI: 10.1186/1759-8753-2-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 06/20/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Determining the mechanisms by which transposable elements move within a genome increases our understanding of how they can shape genome evolution. Class 2 transposable elements transpose via a 'cut-and-paste' mechanism mediated by a transposase that binds to sites at or near the ends of the transposon. Herves is a member of the hAT superfamily of class 2 transposons and was isolated from Anopheles gambiae, a medically important mosquito species that is the major vector of malaria in sub-Saharan Africa. Herves is transpositionally active and intact copies of it are found in field populations of A gambiae. In this study we report the binding activities of the Herves transposase to the sequences at the ends of the Herves transposon and compare these to other sequences recognized by hAT transposases isolated from other organisms. RESULTS We identified the specific DNA-binding sites of the Herves transposase. Active Herves transposase was purified using an Escherichia coli expression system and bound in a site-specific manner to the subterminal and terminal sequences of the left and right ends of the element, respectively, and also interacted with the right but not the left terminal inverted repeat. We identified a common subterminal DNA-binding motif (CG/AATTCAT) that is critical and sufficient for Herves transposase binding. CONCLUSIONS The Herves transposase binds specifically to a short motif located at both ends of the transposon but shows differential binding with respect to the left and right terminal inverted repeats. Despite similarities in the overall structures of hAT transposases, the regions to which they bind in their respective transposons differ in sequence ensuring the specificity of these enzymes to their respective transposon. The asymmetry with which the Herves terminal inverted repeats are bound by the transposase may indicate that these differ in their interactions with the enzyme.
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Affiliation(s)
- Amandeep S Kahlon
- Interdepartmental Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, CA, USA.
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Size matters: versatile use of PiggyBac transposons as a genetic manipulation tool. Mol Cell Biochem 2011; 354:301-9. [PMID: 21516337 DOI: 10.1007/s11010-011-0832-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 04/15/2011] [Indexed: 12/16/2022]
Abstract
Transposons have been promising elements for gene integration, and the Sleeping Beauty (SB) system has been the major one for many years, although there have been several other transposon systems available, for example, Tol2. However, recently another system known as PiggyBac (PB) has been introduced and developed for fulfilling the same purposes, for example, mutagenesis, transgenesis and gene therapy and in some cases with improved transposition efficiency and advantages over the Sleeping Beauty transposon system, although improved hyperactive transposase has highly increased the transposition efficacy for SB. The PB systems have been used in many different scientific research fields; therefore, the purpose of this review is to describe some of these versatile uses of the PiggyBac system to give readers an overview on the usage of PiggyBac system.
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Abstract
Tissue-specific gene expression using the UAS/GAL4 binary system has facilitated genetic dissection of many biological processes in Drosophila melanogaster. Refining GAL4 expression patterns or independently manipulating multiple cell populations using additional binary systems are common experimental goals. To simplify these processes, we have developed a convertible genetic platform, called the Integrase Swappable In vivo Targeting Element (InSITE) system. This approach allows GAL4 to be replaced with any other sequence, placing different genetic effectors under the control of the same regulatory elements. Using InSITE, GAL4 can be replaced with LexA or QF, allowing an expression pattern to be repurposed. GAL4 can also be replaced with GAL80 or split-GAL4 hemi-drivers, allowing intersectional approaches to refine expression patterns. The exchanges occur through efficient, in vivo manipulations, making it possible to generate many swaps in parallel. Furthermore, this system is entirely modular, allowing future genetic tools to be easily incorporated into the existing framework.
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Schistosoma mansoni U6 gene promoter-driven short hairpin RNA induces RNA interference in human fibrosarcoma cells and schistosomules. Int J Parasitol 2011; 41:783-9. [PMID: 21447344 DOI: 10.1016/j.ijpara.2011.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/02/2011] [Accepted: 02/08/2011] [Indexed: 11/21/2022]
Abstract
RNA interference (RNAi) mediated by short hairpin-RNA (shRNA) expressing plasmids can induce specific and long-term knockdown of specific mRNAs in eukaryotic cells. To develop a vector-based RNAi model for Schistosoma mansoni, the schistosome U6 gene promoter was employed to drive expression of shRNA targeting reporter firefly luciferase. An upstream region of a U6 gene predicted to contain the promoter was amplified from genomic DNA of S. mansoni. A shRNA construct driven by the predicted U6 promoter targeting luciferase was assembled and cloned into plasmid pXL-Bac II, the construct termed pXL-BacII_SmU6-shLuc. Luciferase expression in transgenic fibrosarcoma HT-1080 cells was significantly reduced 96 h following transduction with plasmid pXL-BacII_SmU6-shLuc, which encodes luciferase mRNA-specific shRNA. In a similar fashion, schistosomules of S. mansoni were transformed with the SmU6-shLuc or control constructs. Firefly luciferase mRNA was introduced into transformed schistosomules after which luciferase activity was analyzed. Significantly less activity was present in schistosomules transfected with pXL-BacII_SmU6-shLuc compared with controls. The findings revealed that the putative S. mansoni U6 gene promoter of 270 bp in length was active in human cells and schistosomes. Given that the U6 gene promoter drove expression of shRNA from an episome, the findings also indicate the potential of this putative RNA polymerase III dependent promoter as a component regulatory element in vector-based RNAi for functional genomics of schistosomes.
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Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy. BMC Biotechnol 2011; 11:28. [PMID: 21447194 PMCID: PMC3078864 DOI: 10.1186/1472-6750-11-28] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 03/30/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery. RESULTS We have observed that (1) the Tol2 transposase (but not piggyBac) is highly sensitive to molecular engineering; (2) the piggyBac donor with only the 40 bp 3'-and 67 bp 5'-terminal repeat domain is sufficient for effective transposition; and (3) a small amount of piggyBac transposases results in robust transposition suggesting the piggyBac transpospase is highly active. Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. Finally, we have observed that (5) only sites with a particular sequence context can be targeted by either piggyBac or Tol2. CONCLUSIONS The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting.
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Fonager J, Franke-Fayard BMD, Adams JH, Ramesar J, Klop O, Khan SM, Janse CJ, Waters AP. Development of the piggyBac transposable system for Plasmodium berghei and its application for random mutagenesis in malaria parasites. BMC Genomics 2011; 12:155. [PMID: 21418605 PMCID: PMC3073922 DOI: 10.1186/1471-2164-12-155] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 03/20/2011] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The genome of a number of species of malaria parasites (Plasmodium spp.) has been sequenced in the hope of identifying new drug and vaccine targets. However, almost one-half of predicted Plasmodium genes are annotated as hypothetical and are difficult to analyse in bulk due to the inefficiency of current reverse genetic methodologies for Plasmodium. Recently, it has been shown that the transposase piggyBac integrates at random into the genome of the human malaria parasite P. falciparum offering the possibility to develop forward genetic screens to analyse Plasmodium gene function. This study reports the development and application of the piggyBac transposition system for the rodent malaria parasite P. berghei and the evaluation of its potential as a tool in forward genetic studies. P. berghei is the most frequently used malaria parasite model in gene function analysis since phenotype screens throughout the complete Plasmodium life cycle are possible both in vitro and in vivo. RESULTS We demonstrate that piggyBac based gene inactivation and promoter-trapping is both easier and more efficient in P. berghei than in the human malaria parasite, P. falciparum. Random piggyBac-mediated insertion into genes was achieved after parasites were transfected with the piggyBac donor plasmid either when transposase was expressed either from a helper plasmid or a stably integrated gene in the genome. Characterization of more than 120 insertion sites demonstrated that more than 70 most likely affect gene expression classifying their protein products as non-essential for asexual blood stage development. The non-essential nature of two of these genes was confirmed by targeted gene deletion one of which encodes P41, an ortholog of a human malaria vaccine candidate. Importantly for future development of whole genome phenotypic screens the remobilization of the piggyBac element in parasites that stably express transposase was demonstrated. CONCLUSION These data demonstrate that piggyBac behaved as an efficient and random transposon in P. berghei. Remobilization of piggyBac element shows that with further development the piggyBac system can be an effective tool to generate random genome-wide mutation parasite libraries, for use in large-scale phenotype screens in vitro and in vivo.
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Affiliation(s)
- Jannik Fonager
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden. The Netherlands
| | - Blandine MD Franke-Fayard
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden. The Netherlands
| | - John H Adams
- Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida USA
| | - Jai Ramesar
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden. The Netherlands
| | - Onny Klop
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden. The Netherlands
| | - Shahid M Khan
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden. The Netherlands
| | - Chris J Janse
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden. The Netherlands
| | - Andrew P Waters
- Institute of, Infection, Immunity & Inflammation, School of Medical, Veterinary & Life Sciences, & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Scotland, UK
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Li J, Zhang JM, Li X, Suo F, Zhang MJ, Hou W, Han J, Du LL. A piggyBac transposon-based mutagenesis system for the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res 2011; 39:e40. [PMID: 21247877 PMCID: PMC3064801 DOI: 10.1093/nar/gkq1358] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The TTAA-specific transposon piggyBac (PB), originally isolated from the cabbage looper moth, Trichoplusia ni, has been utilized as an insertional mutagenesis tool in various eukaryotic organisms. Here, we show that PB transposes in the fission yeast Schizosaccharomyces pombe and leaves almost no footprints. We developed a PB-based mutagenesis system for S. pombe by constructing a strain with a selectable transposon excision marker and an integrated transposase gene. PB transposition in this strain has low chromosomal distribution bias as shown by deep sequencing-based insertion site mapping. Using this system, we obtained loss-of-function alleles of klp5 and klp6, and a gain-of-function allele of dam1 from a screen for mutants resistant to the microtubule-destabilizing drug thiabendazole. From another screen for cdc25-22 suppressors, we obtained multiple alleles of wee1 as expected. The success of these two screens demonstrated the usefulness of this PB-mediated mutagenesis tool for fission yeast.
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Affiliation(s)
- Jun Li
- National Institute of Biological Sciences, Beijing 102206, China
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